Digital PCR (dPCR) is a simple, rapid, yet accurate technology for non-invasive prenatal testing ([1], [2], [3], [4]). However, there has not been any well-established statistical tool for designing a dPCR experiment in this application. Some existing methods (e.g. [1] and [7]) have not considered important quantities specific in this application.
For example, reference [1] provides a method to estimate number of partitions assuming the proportion of positive compartment is ⅓ in order to detect aneuploidy at 5% false positive rate. Among other things, their method does not consider false negative rate, and does not consider a pre-amplification step. Reference [7] provides a formula for dPCR precision (minimum difference in concentration that can be reliably detected with less than 1% false positive and less than 1% false negative). Their context is in SNV detection and copy number difference, and they do not consider fetal fraction. They do not consider a pre-amplification step either.
Accordingly, improved systems and methods for designing a dPCR experiment for prenatal testing are needed.